A Government MP has hit out at the trade deal struck by Prime Minister Tony Abbott with his Japanese counterpart yesterday, questioning the value of an agreement that does not have a "significant benefit for Australian agriculture".

Acting Prime Minister Warren Truss says the deal with Japan will disappoint some farmers, but should be seen as a "historic step forward" in the economic relationship between the two nations.

But Queensland Liberal National MP George Christensen, who represents the sugar-growing region of Mackay, has told the ABC he is "disappointed there has been no improvement for the sugar industry" which he says "always seems to be on the outer" when it comes to free trade agreements.

"There are some benefits for beef and horticulture in the Japan FTA," the Member for Dawson said.

"But a few sectors does not make up the entire agricultural industry.

"I appreciate that negotiating FTAs, particularly with Japan, is tricky business. But I wonder about the value of an FTA with any nation unless there's significant benefit for Australian agriculture."

Brent Finlay from the National Farmers Federation says the deal "falls short of the mark on a number of fronts" because some tariffs have been only reduced or kept in place instead of eliminated altogether.

"The agreement does not improve, or marginally improves, market access and terms of trade for a number of sectors such as dairy, sugar, grains, pork and rice," Mr Finlay said in a statement.

Mr Abbott and his Japanese counterpart, Shinzo Abe, struck the deal in Tokyo yesterday, saying it would deliver cheaper cars and electronic goods to Australians while opening up Japan's beef and wine markets to Australian businesses.

The hefty 38.5 per cent tariff Japan imposes on Australian beef products will be halved to 19.5 per cent for frozen beef.

The cut will be phased in over 18 years, with an 8 per cent reduction in the first year.

The duty will be higher for fresh beef, at 23.5 per cent, and the cuts will be phased in over 15 years with an immediate 6 per cent reduction in the first year.

Acting Opposition Leader Penny Wong said that was a "very long timeframe" for reductions in Japan's "very high" tariffs on beef.

"The Government has negotiated a far less beneficial agreement with Japan than it negotiated with Korea," Senator Wong told the ABC.

But Mr Truss says beef producers will be "pleased" with the long-awaited reductions in tariffs.

"This agreement doesn't achieve everything that the farm sector would wish, but there are very substantial gains across most sectors of agriculture," Mr Truss told reporters in Sydney.

"When you're doing trade deals, there always has to be some element of give and take. We can't get everything that we would like. Clearly, I would like to see all agricultural trade barriers removed."

Mr Truss says the deal will be reviewed every five years, which "might eventually" lead to "genuinely free and open trade".

More cheese exports but tariffs remain

Australia has won the right to export 20,000 tonnes of cheese but there has been no change to the duties which are currently imposed.

And restrictions placed on Australian imports mean any Australian cheese sold in Japan would have to mixed with Japanese cheese first, which has left the industry pessimistic about any real overall benefits.

Federal Government backbencher and rural Liberal MP Dan Tehan says the increased quota is "beneficial" but a tariff reduction would have been an "excellent outcome".